title: XB001: Shortening of membrane lipid acyl chains compensates for phosphatidylcholine deficiency in choline‐auxotroph yeast

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: Phosphatidylcholine (PC) is an abundant membrane lipid component in most eukaryotes including  yeast. PC has been assigned a multitude of functions in addition to that of building block of the lipid bilayer. Here we show that PC is evolvable essential in yeast by isolating suppressor mutants devoid of PC that exhibit robust growth. The requirement for PC is suppressed by monosomy of chromosome XV, or by a point mutation in the ACC1 gene encoding acetyl-CoA carboxylase. Although these two genetic adaptations rewire lipid biosynthesis differently, both decrease Acc1 activity thereby reducing the average acyl chain length. Accordingly, soraphen A, a specific inhibitor of Acc1, rescues a yeast mutant with deficient PC synthesis. In the aneuploid suppressor, up-regulation of lipid synthesis is instrumental to accomplish feed-back inhibition of Acc1 by acyl-CoA produced by the fatty acid synthase (FAS). The results show that yeast regulates acyl chain length by fine-tuning the activities of Acc1 and FAS, and indicate that PC evolved by benefitting the maintenance of membrane fluidity.

overall_design: Two independent colonies of the wild type control, suppressors and corresponding parental knock-out strain were grown to early midlog and used for transcription profiling by dual-channel microarray against a common reference, consisting of pooled wild type RNAs. The second replicate was analyzed in dye-swap.

first: Xue

last: Bao

first: Martijn

last: Koorengevel

first: Muriel

last: Mari

middle: J

first: Willie

last: Geerts

first: Frank

last: Holstege

first: Christian

last: Klose

first: Amir

last: Homavar

first: Amrah

last: Weijn

first: Stefan

last: Crielaard

first: Mike

last: Renne

first: Anton

middle: I

last: de Kroon

first: Joseph

last: Lorent

first: Michal

middle: A

last: Surma


title: Inhibition of viral suppressor of RNAi proteins by designer peptides protects from enteroviral infection in vivo

status: Public on Jul 31 2021

city: Wuhan

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

country: China

institute: Wuhan institue of virology, CAS

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA interference (RNAi) is an antiviral immunity conserved in diverse eukaryotes including mammals, while viruses encodes viral suppressors of RNAi (VSRs) as countermeasures. However, the physiological impact of RNAi on viral infection in mammals has not been fully assessed, and it also remains unknown whether antiviral RNAi can be therapeutically exploited. Here, we show that peptides designed to target enterovirus A71 (EV-A71)-encoded protein 3A, a well-characterized VSR, triggered an effective antiviral response. These VSR-targeting peptides, particularly ER-DRI, abrogated the VSR function of 3A, which enabled EV-A71-derived siRNA production and unlocked RNAi response that potently inhibited EV-A71 infection in mammals. ER-DRI treatment elicited a strong in vivo antiviral RNAi response that protected mice against lethal EV-A71 challenge. It also potently inhibited another enterovirus, Coxsackievirus-A16, dependently of RNAi. Our findings demonstrate that antiviral RNAi does have a physiologically important impact in mammals and targeting VSRs is a promising strategy for antiviral therapies.

overall_design: Small RNA profile of virus-infected cells

first: Yuan

last: Fang

first: Zezhong

last: Liu

first: Jing

last: Kong

first: Yuhong

last: Fu

first: Yujie

first: Chong

last: Wang

first: Jia

last: Quan

first: Qian

first: Wei

last: Xu

first: Lei

last: Yin

first: Jie

last: Cui

first: Yi

first: Stephen

last: Curry

first: Shibo

last: Jiang

first: Lu

last: Lu

first: Xi

last: Zhou


title: Transcriptome profiling of neutrophils in curdlan-injected Wild Type SKG mice and Mif KO (Mif -/-)  SKG mice

city: Toronto

first: Akihiro

last: Nakamura

state: Ontario

address: 399 Bathurst Street

country: Canada

institute: University Health Network

type: Expression profiling by high throughput sequencing

summary: The curdlan-injected SKG mouse is a mouse model of spondyloarthritis. We identified neutrophils are one of the major immune cells produing MIF in the SKG mice. In this study, we performed total RNA sequecing analysis to identify differentially expressed protein-coding genes (DEGs) in neutrophils isolated from wild type SKG mice comapred to neutrophils isolated from Mif -/- SKG mice after curdlan treatment.

overall_design: 4 samples analyzed, 2 neutrophil RNA samples from Wild Type SKG mice and 2 neutrophil RNA samples from MIf KO (Mif -/-) SKG mice.

first: Igor

last: Jurisica

first: Sayaka

first: Nigil

last: Haroon


title: Progesterone receptor signaling is inhibited by hypermethylation in leiomyoma stem cells to maintain stemness

status: Public on Aug 01 2021

city: Chicago

first: Shimeng

state: Illinois

address: 320 East Superior Street

country: USA

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Sex-Dependent Changes of miRNA Levels in the Hippocampus of Adrenalectomized Rats Following Acute Corticosterone Administration

city: Independencia

first: Wladimir

middle: Antonio

last: Corrales

address: Olivos 1007

department: Biochemistry and Molecular Biology

country: Chile

institute: Universidad de Chile

summary: We explored sex-biased effects of the primary stress glucocorticoid hormone corticosterone on the miRNA expression profile in the rat hippocampus. Adult adrenalectomized (ADX) female and male rats received a single corticosterone (10 mg/kg) or vehicle injection and after 6 h, hippocampi were collected for miRNA, mRNA and Western blot analyses. miRNA profiling microarrays showed a basal sex-biased miRNA profile in ADX rat hippocampi. Additionally, acute corticosterone administration triggered a sex-biased differential expression of miRNAs derived from genes located in several chromosomes and clusters on the X and 6 chromosomes. Putative promoter analysis unveiled that most corticosterone-responsive miRNA genes contained motifs for either direct or indirect glucocorticoid actions in both sexes. The evaluation of transcription factors indicated that almost 50 % of miRNA genes sensitive to corticosterone in both sexes was under glucocorticoid receptor regulation. Transcription factor-miRNA regulatory network analyses identified several transcription factors that regulate, activate or repress miRNA expression. Validated target mRNA analysis of corticosterone-responsive miRNAs showed a more complex miRNA-mRNA interaction network in males compared to females. Enrichment analysis revealed that several hippocampal-relevant pathways were affected in both sexes, such as neurogenesis and neurotrophin signaling. The evaluation of selected miRNA targets from these pathways displayed a strong sex difference in the hippocampus of ADX-vehicle rats. Corticosterone treatment did not change the levels of the miRNA targets and their corresponding tested proteins. Our data indicate that corticosterone exerts a sex-biased effect on hippocampal miRNA expression, which may engage in sculpting the basal sex differences observed at higher levels of hippocampal functioning.

overall_design: Male (n=9) and female (n=9) rats underwent bilateral adrenalectomy (ADX) surgery under isofluorane anesthesia. Seven days after surgery, six ADX animals from each sex were injected with CORT previously dissolved in ethanol and then diluted in saline (10 mg/kg, i.p.). The remaining ADX animals were injected with vehicle (ethanol solution diluted in saline). Considering that GCs promote genomic actions, we chose to euthanize the animals 6 h post-injection as a period in which it is highly probable to observe the effects of the hormone. At the time of sacrifice, trunk blood was collected for the determination of serum CORT levels. Hippocampi were rapidly dissected and flash-frozen in liquid nitrogen and kept at -80 °C until processing for RNA isolation. Frozen hippocampal tissue was disrupted using an UltraTurrax homogenizer in QIAzol Lysis Reagent (Qiagen, California, USA). Enriched RNA fractions of less than 200 nucleotides were then obtained by using the RNeasy Mini Kit (Qiagen, California, USA), followed by the RNeasy MinElute Cleanup Kit After labeling the RNAs with the Affymetrix FlashTagTMBiotin H.S.R. kit, samples were hybridized on Affymetrix GeneChipTM Version 3 miRNA arrays (680 mature and 486 pre-miRNA rat probe sets), according to the Affymetrix hybridization protocols. Array slides were then stained with streptavidin/phycoerythrin, and after washing, they were scanned using the Affymetrix GCS 3000 7G and GeneChip® Operating Software (AGCC; Version 3.2). We used 3 experimental replicas for each sex, including ADX-vehicle and CORT administration.

first: Juan

middle: P

last: Silva

first: Claudio

middle: S

last: Parra

first: Felipe

last: Olave

last: Aguayo

first: Luciano

last: Román-Albasini

first: Esteban

last: Aliaga

first: Leslye

last: Venegas-Zamora

first: Ana

middle: M

last: Ávalos

first: Paulina

last: Rojas

first: Vinicius

last: Maracaja-Coutinho

first: Robert

middle: H

last: Oakley

first: John

last: Cidlowski

first: Jenny

middle: L

last: Fiedler


title: Transgenesis of mammalian PABP reveals new role of mRNA polyadenylation in general stress response in Escherichia coli

city: Trivandrum

first: Rakesh

last: Laishram

state: Kerala

address: Thycaud P O, Poojappura

department: Cardiovascular and Diabetes Biology Group

country: India

institute: Rajiv Gandhi Centre for Biotechnology(RGCB)

summary: To determine the total mRNA polyadenylated in E.coli, we transexpressed mammalian nuclear poly(a) binding protein in E.coli through plasmid and chromosomal integration. RNA Seq analysis revealed general upregulation of around 600 genes commonly in between chrosomal MG PABP and plasmid PABP. 32% of the commonly upregulated genes fall into stress response mRNAs.

overall_design: E.coli K-12 MG 1655 cells were transformed with pBAD PABP for plasmid based PABP expression. Chromosomal integration of PABP was achieved using λ phage. Cells were grown up to OD600=0.5 and is harvested to isolate RNA for the same.

first: Nimmy

last: Francis


title: Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [RNA-seq]

city: Basel

first: Shalu

last: Jhanwar

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: Understanding the origin of morphological diversity across vertebrates is central to evolutionary developmental biology. cis-regulatory elements (CRE) such as enhancers and promoters interpret precise spatiotemporal cues to control and coordinate gene expression. To get insights into both conserved and species-specific variations during early limb patterning and outgrowth, we leverage genome-wide comprehensive assessment of chromatin accessibility and transcriptional changes during mouse forelimb and chicken wing bud development. Our analysis reveals temporal modulation of chromatin accessibility and expression as well as their temporal relationship during the progression of mouse forelimb and chicken wing bud development. Transcription factor binding site enrichment analysis and putative TF occupancy as inferred by integrating TF binding motifs and chromatin accessibility information reveal temporal TF-DNA interactions during forelimb/wing bud patterning. Finally, the integration of accessibility, expression, and TF binding site information allowed to identify candidate gene targets of HAND2 and GLI3 that include conserved as well as species-specific transcriptional regulator-gene interactions.

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: RNA-seq analysis of developing mouse forelimb and chicken wing buds

first: Aimee

last: Zuniga

first: Rolf

last: Zeller


title: SPOP mutations derived from prostate cancer establish a DNA hypermethylation epigenome through stabilizing GLP histone methyltransferase [methylation array]

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

type: Methylation profiling by genome tiling array

summary: Abnormal DNA methylation is one of the major factors driving oncogenesis and therapy resistance in cancer. The CULLIN3-RBX1 E3 ubiquitin ligase adaptor gene SPOP is the most frequently mutated gene in primary prostate cancers (PCa). SPOP-mutated prostate tumors strikingly associate with strongly elevated levels of genome-wide DNA hypermethylation, although the underlying mechanism remains elusive.We use Illumina Infinium MethylationEPIC BeadChip to depict DNA methylation in control and SPOP F102C stabily expressed 22Rv1 cells. Genomic DNA of cells are extracted and quantified by PicoGreen, followed by Illumina Infinium arrays. We find that SPOP mutant expression increases not only the overall cellular level of DNA methylation, but also specifically at loci of a subset of tumor suppressor genes (TSG) including FOXO3 and NDRG1, and this effect is mediated by GLP/G9a binding with DNMT proteins.These findings reveal a previously uncharacterized mechanism by which SPOP mutations promote DNA hypermethylation through stabilization GLP as a chromatin recruiter of DNMT. Our results also suggest that targeting DNA hypermethylation is a viable strategy for effective management of SPOP mutated PCa.

overall_design: Examination of DNA methylation in SPOP WT and SPOP F102C Pca cell line

first: Haojie

last: Huang

first: Jianong

last: Zhang

first: Liguo

last: Wang


title: Schizophrenia risk candidate EGR3 is a novel transcription factor of RELN and regulates neurite outgrowth via the Reelin signal pathway in vitro

city: Xi'an

first: Fayi

last: Nie

state: China

address: YanTa Road 76

institute: Xi’an Jiaotong University Health Science Center

summary: Schizophrenia is a severe psychiatric disorder with a strong hereditary component that affects approximately 1% of the world’s population. The disease is most likely caused by the altered expression of a number of genes that function at the level of biological pathways or gene networks. Transcription factors (TF) are indispensable regulators of gene expression. EGR3 is a TF associated with schizophrenia. In the current study, DNA microarray and ingenuity pathway analyses (IPA) demonstrated that EGR3 regulates Reelin signaling pathway in SH-SY5Y cells. ChIP and luciferase reporter studies confirmed that EGR3 directly binds to the promoter region of RELN thereby activating RELN expression. Both the expression of EGR3 and RELN were decreased during neuronal differentiation induced by retinoic acid (RA) in SH-SY5Y cells, and EGR3 overexpression reduced neurite outgrowth which could be partially reversed by the knockdown of RELN. The expression levels of EGR3 and RELN in peripheral blood of patients with schizophrenia were found to be downregulated (compared to healthy controls), and were positively correlated. Furthermore, data mining from public databases revealed that the expression levels of EGR3 and RELN were presented a positive correlation in postmortem brain tissue of schizophrenic individuals. Taken together, the current study suggests that EGR3 is a novel TF of the RELN gene and regulates neurite outgrowth via Reelin signaling pathway. Our findings contribute to the understanding of the regulatory role of EGR3 in the pathophysiology and molecular mechanisms of schizophrenia, and potentially to the development of new therapies and diagnostic biomarkers for the disorder.

overall_design: Lentiviral particles for EGR3 overexpression (OE) and negative control (NC) were used to infect SH-SY5Y cells. Three biological replicates collected from each group were subjected to microarray analysis.

first: Jie

last: Ma


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Wild Type and invF Deficient Mutant of  Pseudomonas fluorescens 2P24

status: Public on Aug 03 2021

city: Beijing

first: Jing

state: Not applicable

address: 12 Zhongguancun South St

institute: Chinese Academy of Agricultural Sciences

summary: InvF, an AraC-type transcriptional activator, regulated the expression of genes that encoded the secreted effector molecules SipABCD, SigD, SptP, and SopE in Salmonella typhimurium. However, it seems that almost all effector homologs were lost in P. fluorescens 2P24. To identify the InvF regulon in strain 2P24, the invF deficient mutant 2P24ΔinvF was constructed, and we implemented transcriptome sequencing (RNA-seq). Both of strains 2P24 and 2P24ΔinvF were incubated in mannitol-glutamate (MG) minimal medium at 28℃ for 6 h and 12 h. The cell fractions were separated by centrifugation at 10, 000 rpm for 5 min at 4°C. Total RNA was isolated using a E.Z.N.A.® Bacterial RNA Kit (Omega Bio‐tek, USA) as described by the manufacturer for RNA-seq. mRNA profiles of strains 2P24 and 2P24ΔinvF were generated by deep sequencing, in triplicate, using Illumina Hiseq. A total of 127 significantly differentially expressed genes (DEGs) were obtained by comparing the transcriptional level of strain 2P24ΔinvF with 2P24 at 6 h and 12 h [Fold change ≥ 1.5; p value ≤ 0.05]. Fifty-two down-regulated genes were regarded as InvF regulon candidates. Among the InvF regulon candidates, 39 genes were screened based on their gene functional annotation for qRT-PCR verification. Finally, eight genes were confirmed to be regulated positively by InvF. They encoded dihydrolipoyl dehydrogenase, toxin-activating lysine-acyltransferase, phage infection protein, AsnC family protein, two hypothetical proteins, NAD(P)H dehydrogenase, and protein IolH, respectively.

overall_design: mRNA profiles of strains 2P24 and 2P24ΔinvF which were incubated in mannitol-glutamate (MG) minimal medium at 28℃ for 6 h and 12 h.

first: Hai-Lei

last: Wei


title: Genome-wide transcriptome regulation by progesterone receptor in primary leiomyoma cells

first: Shimeng

last: Liu

summary: Uterine leiomyomas (LM) affect up to 80% of all reproductive-age women. LM growth requires progesterone, progesterone receptor (PGR), and the maintenance and proliferation of a small (5%) stem cell population. Stem cell activation and differentiation are driven by DNA methylation and nuclear hormone receptor action, but crosstalk between these mechanisms remains unclear. We performed an integrated analysis of the transcriptome and epigenetic landscape of LM cells at three differentiation stages and the PGR cistrome of whole LM tissue. The PGR-deficient stem cell population harbored a unique methylation landscape, with hypermethylation at the PGR gene locus and PGR-binding regions, which suppressed stem cell responsiveness to progesterone. The DNA methylation inhibitor 5’-Aza upregulated the expression of PGR and its target genes by stimulating PGR recruitment to the targeted gene loci, and significantly depleted the LM stem cell population and its tumor-initiating capacity.  We herein provided mechanistic insights via therapeutically accelerating the stem cell differentiation process of a hormone-sensitive tumor.

overall_design: Identify transcriptome changes between siCtrl and siPGR in  primary LM cells using RNA-Seq

first: Ping

last: Yin

first: Serdar

last: Bulun


title: Genome-wide prgesterone receptor binding profile in human uterine leiomyoma tissue

overall_design: Genome-wide PGR binding profiling in human LM tissue using ChIP-Seq


title: Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development


title: High Light and High Temperature Reduce Photosynthetic Efficiency via Different Mechanisms in the C4 Model Setaria viridis

city: St. Louis

first: Ru

state: Missouri

address: 95 N Warson Rd

institute: Donald Danforth Plant Science Center

summary: C4 plants frequently experience damaging high light (HL) and high temperature (HT) conditions in native environments, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4 model plant Setaria viridis responded to a four-hour HL or HT treatment at the photosynthetic, transcriptomic, and ultrastructural levels. Although we observed a comparable reduction of photosynthetic efficiency in HL- or HT-treated leaves, detailed analysis of multi-level responses revealed important differences in key pathways and M/BS specificity responding to HL and HT. We provide a systematic analysis of HL and HT responses in S. viridis, reveal different acclimation strategies to these two stresses in C4 plants, discover unique light/temperature responses in C4 plants in comparison to C3 plants, and identify potential targets to improve abiotic stress tolerance in C4 crops.

overall_design: Transcriptomic time-course analysis of 4h high light or high temperature treated Setaria viridis leaves

first: Cheyenne

last: Anderson

first: Erin

last: Mattoon

first: Ningning

last: zhang

first: Eric

last: Becker

first: William

last: McHargue

first: Jiani

last: Yang

first: Dhruv

last: Patel

first: Oliver

last: Dautermann

first: Scott

last: McAdam

first: Tonantzin

last: Tarin

first: Sunita

last: Pathak

first: Tom

last: Avenson

first: Jeffrey

last: Berry

first: Maxwell

last: Braud

first: Krishna

middle: K

last: Niyogi

first: Margaret

last: Wilson

first: Dmitri

last: Nusinow

first: Rodrigo

last: Vargas

first: Kirk

last: Czymmek

first: Andrea

last: Eveland


title: cis-regulation of Grem1 during limb development [ChIP-seq]

first: Shalu

last: Jhanwar

summary: Chromatin immunoprecipitation in combination with sequencing (ChIP-seq) was used to identify the interactions of CRMs with key regulators of Grem1 expression, namely SMAD4 (mediating response to BMP signal transduction) and  GLI3 (SHH signal transduction). This analysis revealed the presence of a single significantly enriched SMAD4 ChIP-seq peak in CRM2 during initiation of forelimb bud development, when BMP4 is required to initiate/upregulate the Grem1 transcription. During progression of limb development, GLI3 chromatin complexes interact with all enhancers except CRM5. which agrees with the predominant role of SHH-mediated Grem1 regulation during outgrowth and/or GLI3R-mediated repression during termination. Thus, the Grem1 TAD encodes an array of CRM enhancers that integrate inputs from BMP and SHH signaling into the dynamic regulation of Grem1 during limb bud outgrowth.

overall_design: ChIP-Seq of Smad4 and Gli3 on whole embryo and embryonic limb bud.

first: Kevin

last: Peterson

first: Aimée

last: Zuniga

first: Rolf

last: Zeller


title: Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [ATAC-seq]

overall_design: ATAC-seq analysis of developing mouse forelimb and chicken wing buds. Raw data of E10.5 and E11.5 developmental stages were previously submitted in GEO under GSE126292 (GSM3595750-GSM3595753).

first: Aimee


title: Systematic Analysis of Long Intergenic Non-Coding RNAs in C. elegans Germline Uncovers Roles in Somatic Growth

city: Jerusalem

first: Yonatan

last: Tzur

address: Givat-Ram

country: Israel

institute: Hebrew University of Jerusalem

summary: Long intergenic non-coding RNAs (lincRNAs) are transcripts longer than 200 nucleotides that are transcribed from non-coding loci yet undergo biosynthesis similar to coding mRNAs. The disproportional number of lincRNAs expressed in testes suggests that lincRNAs are important during gametogenesis, but experimental evidence has implicated very few lincRNAs in this process. We took advantage of the relatively limited number of lincRNAs in the genome of the nematode Caenorhabditis elegans to systematically analyse the functions of lincRNAs during meiosis. We deleted six lincRNA genes that are highly and dynamically expressed in the C. elegans gonad and tested the effects on central meiotic processes. Surprisingly, whereas the lincRNA deletions did not strongly impact fertility, germline apoptosis, crossovers, or synapsis, linc-4 was required for somatic growth. Slower growth was observed in linc-4-deletion mutants and in worms depleted of linc-4 using RNAi, indicating that linc-4 transcripts are required for this post-embryonic process. Unexpectedly, analysis of worms depleted of linc-4 in soma versus germline showed that the somatic role stems from linc-4 expression in germline cells. This unique feature suggests that some lincRNAs, like some small non-coding RNAs, are required for germ-soma interactions

overall_design: CRISPR deletion of linc genes in C. elegans. Compartive transcriptomics of linc-4 to WT

first: Hasan

last: Ishtayeh

first: Hanna

last: Achache

first: Eitan

last: Kroizer

first: Yisrael

first: Eyal

last: Itskovits

first: Hila

last: Gingold

first: Corinne

last: Best

first: Oded

last: Rechavi

middle: B


title: Connection of core and and tail Mediator modules restrains transcription from TFIID-dependent promoters [ChEC-seq Med16-AID]

status: Public on Jul 30 2021

city: Bloomington

first: Gabriel

middle: E

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

summary: The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels PIC formation at SAGA-requiring and TFIID-dependent genes. We suggest that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.

overall_design: ChEC-seq of Mediator subunits in Med16 deletion or depletion strains.

first: Moustafa

last: Saleh


title: cis-regulation of Grem1 during limb development


title: cis-regulation of Grem1 during limb development [4C-seq]

summary: Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. In this study, we identified cis regulatory modules (CRMs) within the Fmn1/Grem1 cis-regulatory landscape that participate in controlling spatiotemporal expression of Grem1. We generated different Grem1 alleles lacking either individual CRMs, combinations or entire enhancer clusters (EC1 and EC2) using CRISPR/Cas genome editing. To study potential interactions of these CRMs with the Grem1 promoter, we generated 4C-seq profiles of different alleles. Our analysis of 4C-seq shows that the overall structure of the Grem1 TAD is maintained in CRM2-/- and EC1-/- forelimb buds. Similar to EC1, the chromatin architecture of the Grem1 TAD is not disrupted outside the EC2 and EC1EC2 deletions. In all the genotypes, the contacts of the promoter with the remainder of the Grem1 TAD  are rather increased. Thus, our results revealed that the spatio-temporal changes in Grem1 expression are caused by cis-regulatory alterations due to the deletions of EC1 and EC2 and not global changes in chromatin architecture.

overall_design:
Circular Chromosome Conformation Capture (4C seq) at Grem1 locus in developing limbs of mutants and WT at E11

Deletion coordinates (mm10) of mutants used in this study:
del CRM2: chr2:113689537-113699485
del EC1: chr2:113636776-113707974
del EC2: chr2:113572310-113606580
del EC1 and EC2: chr2:113636776-113707974 and chr2:113572310-113606580
del Cis: chr2:113528475-113709592

first: Laurène

last: Ramos Martins

first: Jonas

last: Malkmus


title: Transcriptional and Epigenetic analysis of IRF4-deficient B cell differentiation

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University


title: The pan HDAC inhibitor Givinostat improves muscle function and histological parameters in two Duchenne Muscular Dystrophy murine models expressing different haplotypes of the LTBP4 gene.

city: Cinisello Balsamo

first: Simonetta

middle: Andrea

last: Licandro

state: MI

address: Via Dei Lavoratori, 54

country: Italy

institute: ITALFARMACO SPA

summary: Background: In the search of genetic determinants of Duchenne Muscular Dystrophy (DMD) severity, LTBP4, a member of the latent TGF-β binding protein family, emerged as an important predictor of functional outcome trajectories in mice and humans. Nonsynonymous single nucleotide polymorphisms in LTBP4 gene associate with prolonged ambulation in DMD patients, whereas an in-frame insertion polymorphism in the mouse LTBP4 locus modulates disease severity in mice by altering proteolytic stability of the Ltbp4 protein and release of transforming growth factor-β (TGF-β). Givinostat, a pan-histone deacetylase inhibitor currently in phase III clinical trials for DMD treatment, significantly reduces fibrosis in muscle tissue and promotes the increase of cross sectional area (CSA) of muscles in mdx mice. In this study we investigated the activity of Givinostat in mdx and in D2.B10 mice, two mouse models expressing different Ltbp4 variants and developing mild or more severe disease as a function of Ltbp4 polymorphism.  Methods: Givinostat and steroids were administrated for 15 weeks in both DMD murine models and their efficacy was evaluated by grip strength and run to exhaustion functional tests. Histological examinations of skeletal muscles were also performed to asses the percentage of fibrotic area and CSA increase.  Results: Givinostat treatment increased maximal normalized strength to levels that were comparable to those of healthy mice in both DMD models. The effect of Givinostat in both grip strength and exhaustion tests was dose-dependent in both strains and, in D2.B10 mice, Givinostat outperformed steroids at its highest dose. The in vivo treatment with Givinostat was effective in improving muscle morphology in both mdx and D2.B10 mice by reducing fibrosis.  Conclusion: Our study provides evidence that Givinostat has a significant effect in ameliorating both muscle function and histological parameters in mdx and D2.B10 murine models suggesting a potential benefit also for patients with a poor prognosis LTBP4 genotype.

overall_design: Plasma samples that were analyzed were from: wild type (wt) mice (C57BL/10J; n = 3), dystrophin deficient mice (C57BL10ScSn-Dmdmdx/J or mdx) untreated (naive mdx; n = 3) or treated with both vehicle (n = 4) and Givinostat at 37.5 mg/kg (n = 3)

first: Luca

last: Crippa

first: Roberta

last: Pomarico

first: Raffaella

last: Perego

first: Gianluca

last: Fossati

first: Flavio

last: Leoni

first: Christian

last: Steinkühler


title: Connection of core and and tail Mediator modules restrains transcription from TFIID-dependent promoters [nsRNA-seq]

overall_design: nsRNA-seq of auxin-inducible degron strains treated with DMSO or 3-IAA


title: Exercise during pregnancy prevents parental obesity-induced decline of metabolic function in adult offspring [Bisulfite-Seq]

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: It is known that both maternal and paternal health/disease can influence the early development and later metabolic homeostasis of the offspring. We investigated whether maternal exercise during gestation alone could protect the offspring from the adverse effects of either maternal or paternal obesity induced by high-fat diet (HFD). To understand the underlying mechanisms we performed transcriptomics, whole-genome DNA methylation and targeted DNA methylation analysis at the metabolic master regulator, peroxisome proliferator-activated receptor g coactivator-1a (Pgc-1a) promoter in the adult offspring skeletal muscle. Both maternal and paternal HFD resulted in impaired glucose tolerance in the offspring at 9 months of age. Maternal exercise during gestation completely mitigated this metabolic impairment induced by either maternal or paternal HFD. Adult offspring exposed to either maternal or paternal HFD without exercise during gestation had skeletal muscle transcriptional profiles enriched in genes regulating inflammation and immune responses, whereas maternal exercise resulted in a transcriptional profile that was more similar to control offspring from normal chow fed parents. Changes in promoter and CpG DNA methylation were detected between the groups but did not explain the transcriptional changes. Maternal HFD increased methylation of the Pgc-1α promoter at CpG -260, which was prevented by maternal exercise. Paternal HFD did not affect the methylation of the Pgc-1α promoter. These findings demonstrate the negative consequences of maternal and paternal obesity for the offspring’s metabolic outcomes later in life and the clear benefits of maternal exercise during gestation. The mechanisms involve transcriptional regulation of skeletal muscle likely through multiple types of epigenetic modifications.

overall_design: 4-8 Samples analyzed per group. Control group is NC-Sed-MP

first: Rhianna

middle: C

last: Laker

last: Altıntaş

first: Zhen

last: Yan

first: Romain

last: Barres


title: Connection of core and and tail Mediator modules restrains transcription from TFIID-dependent promoters

last: Zentner

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae W303

overall_design: Refer to individual Series


title: IRF4-dependent division-coupled reprogramming events [IRF4cKO.RNAseq]

summary: To assess the timing and scope of IRF4–dependent reprogramming in vivo, CTV-labeled IRF4–sufficient and –deficient B cells were transferred into mMT hosts. One day later, hosts were challenged with 50 mg LPS. Three days post-LPS challenge, transferred cells were recovered and sorted from divisions 0, 1, 3, 4, 5, and 6 as determined by CTV dilution for RNA–seq.

overall_design: RNA-seq on control and IRF4-deficient B cells at discrete divisions

first: C

middle: D

first: D

middle: G

last: Patterson

first: J

last: Boss


title: SUDHL4 cells

city: New York

first: David

last: Dominguez-Sola

state: NY

address: One Gustave L. Levy Place, Box 1044A

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai


title: Transcriptional profiling of SUDHL4 cells edited by CRISPR-cas9 to induce point mutations in the FOXO1 locus

summary: The transcription factor FOXO1 directs germinal center (GC) polarity and supports affinity maturation by silencing immune activation programs in GC B cells. Recurrent somatic mutations in GC-derived B cell non-Hodgkin lymphomas (B-NHL) often target and reportedly activate FOXO1 by preventing its negative regulation by PI3K. Herein, using ad hoc mouse models, engineered cell lines and primary tumor specimens, we show instead that FOXO1 mutant proteins display altered transcriptional activities suggestive of partial loss-of-function. These defects drive simultaneous hyperactivation of signaling pathways (Stress Activated Protein Kinase -SAPK/JNK, Phosphoinositide 3-kinase -PI3K/AKT) and gene expression programs typically activated in GC B cells upon positive selection. Such changes confer mutant B cells with competitive advantages in response to key immune signals, leading to abnormal amplification of GC responses. Evidence of these FOXO1 ‘mutant’ gene programs can be found in a fraction of human B-NHL and predict clinical outcome, thus implying the frequent co-option of positive selection programs during GC-derived B-NHL pathogenesis.

overall_design: SUDHL4 cells which are normally WT for FOXO1 were edited with CRISPR-Cas9 to intruduce M1L point mutations in homozygosity or S22P point mutations in heterozygosity. Singles clones were expanded in culture and profiled by RNA-seq

first: Mark

last: Roberto

first: Antony

last: Holmes


title: Mapping of WT FOXO1 and M1L FOXO1 binding sites in SUDHL4 cells

overall_design: SUDHL4 were edited using CRISPR-Cas9 to introduce biallic M1L mutations in the FOXO1 locus. Two independent single cell clones were expanded in culture and used to compare binding repertoires between WT and M1L FOXO1.

last: Dominuguez-Sola


title: Transcriptional profiling of SUDHL4 cells stimulated with megaCD40L and IgM/G for 24 hours

overall_design: SUDHL4 cells were subjected to combined stimulation with megaCD40L and IgM/G for 24 hours in culture at 37C, 5% CO2


title: Expression data from gastrocnemius muscle of denervated mice ingesting maslinic acid

status: Public on Jul 29 2021

city: Tsukuba

first: Yuki

last: Yamauchi

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary:
Gene expression profiling of the effect of maslinic acid in denervated mice
ICR mice were fed either the diet containing 0.27% maslinic acid and the control diet. After 7 days, the sciatic nerve of both legs was cut and a 5-mm piece was excised under anesthesia. Microarray gene expression profiling was conducted for biological replicates of gastrocnemius muscle after 14 days from denervation surgery.

overall_design: Total RNA of gastrocnemius muscle was isolated using Isogen reagent (Nippon Gene Co., Ltd., Tokyo, Japan) and then purified using the RNeasy Mini Kit (Qiagen K.K., Tokyo, Japan). The quality and quantity of total RNA was measured on NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Japan). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: IRF4-dependent division-coupled reprogramming events [IRF4cKO.ATACseq]

first: Chris

last: Scharer

summary: To assess the timing and scope of IRF4–dependent reprogramming in vivo, CTV-labeled IRF4–sufficient and –deficient B cells were transferred into mMT hosts. One day later, hosts were challenged with 50 mg LPS. Three days post-LPS challenge, transferred cells were recovered and sorted from divisions 0, 1, 3, 4, 5, and 6 as determined by CTV dilution for ATAC–seq.

overall_design: ATAC-seq on control and IRF4-deficient B cells at discrete divisions


title: Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters [ChIP-Seq]

first: Gabriel

summary: The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels of PIC formation at SAGA-requiring and TFIID-dependent genes. We suggest that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.

overall_design: ChIP-seq of Mediator in Wildtype and Med16-deletion

first: Moustafa

last: Saleh

first: Célia

last: Jeronimo

first: François

last: Robert


title: lncRNA and mRNA in a septic acute lung injury mouse model

city: chongqing

first: Liying

last: Zou

address: 136 Zhongshan 2nd

institute: Children's Hspital of ChongQing Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Sepsis is commonly complicated by acute lung injury (ALI). We aimed to determine the long noncoding RNAs (lncRNAs) and mRNAs expression profiles in a cecal ligation and puncture mouse model of septic ALI. The model was verified by the elevation of inflammatory cytokine levels, the protein concentration in Bronchoalveolar lavage fluid and histological analysis of lung tissues. LncRNA and mRNA profiles were detected using an Agilent microarray. Bioinformatic analyses were employed to analyze the expression profiles and multiple biological functions. The results showed that lncRNAs  These results implied that lncRNAs would  be novel regulators and potential targets in septic ALI.

overall_design: we divided  6-8 weeks mice into  two groups - control and septic model and 6 mice per group.

first: Luyun

last: Zhang

first: Xiu

last: Yuan

first: Qing

last: Yu

first: Fang

last: Fang

first: Feng

last: Xu


title: Combined Inhibition of SHP2 and CXCR1/2 Promotes Anti-Tumor T Cell Response in NSCLC

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: SHP2 inhibitors (SHP2i) alone and in various combinations are being tested in multiple tumors with over-activation of the RAS/ERK pathway. SHP2 plays critical roles in normal cell signaling; hence, SHP2is could influence the tumor microenvironment. We found that SHP2i treatment depleted alveolar and M2-like macrophages, induced tumor-intrinsic CCL5/CXCL10 secretion and promoted B and T lymphocyte infiltration in Kras- and Egfr- mutant non-small cell lung cancer (NSCLC). However, treatment also increased intratumor gMDSCs via tumor-intrinsic, NF-kB-dependent production of CXCR2 ligands. Other RAS/ERK pathway inhibitors also induced CXCR2 ligands and gMDSC influx in mice, and CXCR2 ligands were induced in tumors from patients on KRASG12C-inhibitor trials. Combined SHP2(SHP099)/CXCR1/2(SX682) inhibition depleted a specific cluster of S100a8/9high gMDSCs, generated Klrg1+ CD8+ effector T cells with a strong cytotoxic phenotype but expressing the checkpoint receptor NKG2A, and enhanced survival in Kras- and Egfr-mutant models. Our results argue for testing RAS/ERK pathway/CXCR1/2/NKG2A inhibitor combinations in NSCLC patients.

overall_design: To compare gene expression of KP tumor cells, and associated microenviromental changes upon different drug treatments.

first: Kwan

last: Tang

first: Benjamin

last: Neel

first: Kwok-Kin

last: Wong


title: RNA sequencing of control and Dnmt1Δ/Δep knockout keratinocytes at P3

city: Vienna

first: Christian

last: Seiser

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

summary: To investigate whether the effects of DNMT1 ablation in keratinocytes are cell-autonomous in the context of the innate immune response, RNA sequencing was performed using keratinocytes isolated from P3 Dnmt1Δ/Δep and control mice.

overall_design: For RNA sequencing epidermis of three control and three Dnmt1∆/∆ep mice was isolated at P3 and keratinocytes were cultured for 5 days. RNA was and then used for RNA sequencing. The aim was to do the analysis of differentially expressed genes across the two conditions to determine whether the effects of DNMT1 ablation in keratinocytes are cell-autonomous in the context of the innate immune response. Genes that showed a minimum of a 2-fold change in expression levels (adjusted P value of£0.05) were classified as up-regulated, whereas genes displaying a fold change of £ 0.5 (adjusted P value of£0.05) were categorized as down-regulated. The cutoffs for differential expression were set as absolute fold-change >2 and a corrected P-value of >0.05.

first: Mirjam

last: Beck

first: Heinz

last: Fischer

first: Ido

last: Tamir


title: IL-33 causes thermogenic failure in aging by expanding dysfunctional adipose ILC2

first: Maxim

last: Artyomov

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: This SuperSeries is composed of the SubSeries listed below.


title: IL-33 causes thermogenic failure in aging by expanding dysfunctional adipose ILC2 [single cell rnaseq]

summary: Aging impairs the integrated immunometabolic responses which have evolved to maintain core body temperature in homeotherms to survive cold-stress, infections, and dietary restriction. Adipose tissue inflammation regulates the thermogenic stress response but how adipose tissue-resident cells instigate thermogenic failure in the aged are unknown. Here, we define alterations in the adipose-resident immune system and identify that type 2 innate lymphoid cells (ILC2) are lost in aging. Restoration of ILC2 numbers in aged mice to levels seen in adults through IL-33 supplementation failed to rescue old mice from metabolic impairment and increased cold-induced lethality. Transcriptomic analyses revealed intrinsic defects in aged ILC2, and adoptive transfer of adult ILC2 are sufficient to protect old mice against cold. Thus, the functional defects in adipose ILC2 during aging drive thermogenic failure.

overall_design: Unbiased profiling of adipose tissue immune and stromal vascular fractions

first: Emily

last: Goldberg

first: Irina

last: Shchukina

first: Yun-Hee

last: Youm

first: Seungjin

last: Ryu

first: Takeshi

last: Tsusaka

first: Kyrlia

last: Young

first: Christina

last: Camell

first: Tamara

last: Dlugos

middle: N

first: Vishwa

last: Dixit


title: IL-33 causes thermogenic failure in aging by expanding dysfunctional adipose ILC2 [bulk rnaseq]

overall_design: IL-33 was given by ip injection daily for 5 consecutive days to adult and old mice. Then, mice were rested for 6 additional weeks prior to tissue collection and ILC2 isolation from VAT.


title: Exercise during pregnancy prevents parental obesity-induced decline of metabolic function in adult offspring [RNA-Seq]

first: Ali

last: Altintas

overall_design: 3 samples per groups were analyzed. Control in NC-Sed-MP.

first: Rhianna

last: Laker

last: Altıntaş

first: Zhen

last: Yan

first: Romain

last: Barres


title: Metabolic regulation by PD-1 signaling promotes long-lived quiescent CD8 T cell memory in mice

city: Seattle

first: Surojit

last: Sarkar

state: WA

address: 1100 Olive Way, Suite 100

department: Department of Pediatrics and Laboratory Medicine

institute: University of Washington School of Medicine

summary:
Inhibitory signaling in dysfunctional CD8 T cells through the programmed cell death 1 (PD-1) axis is well established in chronic viral infections and cancers. PD-1 is also transiently induced to high concentrations during priming of acute infections and immunizations, yet its impact on the development of long-lived antigen-independent T cell memory remains unclear. In addition to its expected role in restraining clonal effector expansion, here we show that PD-1 expression on antigen-specific CD8 T cells is required for the development of a durable CD8 T cell memory pool after antigen clearance. Loss of T cell-specific PD-1 signaling led to increased contraction and a defect in antigen-independent renewal of memory CD8 T cells in response to homeostatic cytokine signals, thus resulting in attrition of the memory pool over time. Whereas exhausted CD8 T cells regain function after PD-1 checkpoint blockade during chronic viral infection, the pre-existing pool of resting functional bystander memory CD8 T cells established in response to a previously administered immunogen decreased. Metabolically, PD-1 signals were necessary for regulating the critical balance of mTOR-dependent anabolic glycolysis and fatty acid oxidation programs to meet the bioenergetics needs of quiescent memory. These results define PD-1 as a key metabolic regulator of protective T cell immunity. Further, these results have potential clinical implications for pre-existing CD8 T cell memory during PD-1 checkpoint blockade immunotherapy.
We used genomewide microarrays to analyze the mRNA gene expression profile of LCMV GP33-specific effector CD8 T cells from P14 mice that were differentiated in the presence (WT) or absence of PD1 signals (PD1KO) upon in vivo infection with LCMV Armstrong.

overall_design: 4 Groups of FACS purified GP33-specific CD8 T cells were analyzed by Affymetrix microarrays. Group 1 - Naïve Wild Type GP33-specific CD8 T cells from P14 mice; Group 2 - Wild type GP33-specific CD8 T cells isolated at Day 7 post-infection from LCMV Arm infected mice; Group 3 - PD1 Knockout GP33-specific CD8 T cells isolated at Day 7 post-infection from LCMV Arm infected mice; Group 4 - Memory Wild type GP33-specific CD8 T cells isolated at Day >90 post-infection from LCMV Arm infected mice

first: Vandana

last: Kalia


title: Next Generation Sequencing of BMDM overexpressing GFP, IRX3-WT, IRX3-S361A and IRX3-S389A

first: Jingfei

last: Yao

state: State / Province

address: yiheyuan street

institute: Peking university

summary: IRX3 is a transcriptional factor, which play important functions in developmental processes. But the role of IRX3 in immune cells are less studied. So we sequenced mRNA from BMDMs overexpressing GFP,  IRX3, as well as two phosphorylation site mutants-S361A and S389A respectively, to address the roles of IRX3 in macrophages.

overall_design: BMDMs were isolated from Irx3-/- mice and overexpressed with  GFP, IRX3-WT, IRX3-S361A and IRX3-S389A by AAV infection. After 100 ng/ml LPS treatment for 4 h, the cells were collected for RNA extraction.

first: Yifu

last: Qiu


title: Genome-wide DNA demethylation of NB-1 (neuroblastoma cell line) after treatment of mock and 5-aza-2'-deoxycytidine (5-aza-dC)

city: Tokyo

first: Naoko

last: Hattori

address: 5-1-1 Tsukiji, Chuo-ku

department: Research Institute

institute: National Cancer Center

summary: A neuroblasoma cell line, NB-1, was treated with a DNA demethylating agents (5-aza-2'-deoxycytidine: 5-aza-dC). Genome-wide DNA methylation was analyzed using the Infinium HumanMethylation450 BeadChip.

overall_design: Bisulfite converted DNA from the 2 samples were hybridized to the Infinium HumanMethylation450 BeadChip

first: Toshikazu

last: Ushijima


title: Differential gene expression analysis of genes deregulated in Ptch1+/−/Tis21 knockout  vs.  Ptch1+/−/Tis21 wild-type mice

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

institute: IRIB-CNR

summary: We generated a new medulloblastoma model by crossing Patched1 heterozygous mice, which develop medulloblastomas with low frequency, with mice lacking the Tis21 gene. Double knock-out mice show a significant increase in medulloblastoma frequency and hyperplastic EGL lesions formed by preneoplastic GCPs. We found that Tis21 deletion does not affect the proliferation of GCPs but it inhibits their differentiation and their ability to migrate outside the EGL, remaining for a prolonged time in the cerebellum proliferative area. We identified as a drug target and major responsible of this migration defect the down-regulation of the promigratory chemokine Cxcl3 rather than a number of down-regulated tumor inhibitors and up-regulated tumor facilitators, and focusing on pathways potentially involved in the tumorigenesis and on putative new drug targets. Among them, we identified the activation of the PI3K/AKT/mTOR pathway that contributes to medulloblastoma development and to high frequency tumorigenesis when the Tis21 gene is down-regulated. Moreover, we used a novel PI3K inhibitor in nodules derived from primary Ptch1+/−/Tis21KO causing a significant reduction of tumor growth, inhibiting proliferation and increasing apoptosis.

overall_design: Two-condition experiment, cerebellar granule precursor cells (GCPs) of Ptch1+/−/Tis21 knockout  vs.  Ptch1+/−/Tis21 wild-type mice isolated at P7, for each genotype were used four biological replicates.

first: Felice

last: Tirone


title: Sonlicromanol improves neuronal network dysfunction and transcriptome changes linked to m.3243A>G heteroplasmy in iPSC-derived neurons

city: Nijmegen

first: Nael

last: Nadif Kasri

address: Geert Grooteplein Zuid 10

department: Department of Human Genetics

country: Netherlands

institute: Radboudumc

summary: Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) is often caused by an adenine to guanine variant at m.3243 (m.3243A>G) of the MT-TL1 gene. To understand how this pathogenic variant affects the nervous system, we differentiated human induced pluripotent stem cells (iPSCs) into excitatory neurons with normal (low heteroplasmy) and impaired (high heteroplasmy) mitochondrial function from MELAS patients with the m.3243A>G pathogenic variant. We combined micro-electrode array (MEA) measurements with RNA sequencing (MEA-seq) and found reduced expression of genes involved in mitochondrial respiration and presynaptic function, as well as non-cell autonomous processes in co-cultured astrocytes. Finally, we show that the clinical phase II drug sonlicromanol can improve neuronal network activity when treatment is initiated early in development. This was intricately linked with changes in the neuronal transcriptome. Overall, we provide insight in transcriptomic changes in iPSC-derived neurons with high m.3243A>G heteroplasmy, and show the pathology is partially reversible by sonlicromanol.

overall_design: From 2 isogenic sets three replicates from low m.3243A>G heteroplasmy (LH) samples, two replicates from high m.3243A>G heteroplasmy (HH) samles, and three replicates from HH samples treated with sonlicromanol were included.

first: Teun

last: Klein Gunnewiek

first: Anouk

last: Verboven

first: Tamas

last: Kozicz


title: Human autoinflammatory disease reveals ELF4 as a transcriptional regulator of inflammation

city: New Haven

first: Carrie

last: Lucas

state: CT

address: 300 George Street

institute: Yale University

summary: Transcription factors specialized to limit the destructive potential of inflammatory immune cells remain ill-defined. We discovered loss-of-function variants in the X-linked ETS transcription factor gene ELF4 in multiple unrelated male patients with early-onset mucosal autoinflammation and inflammatory bowel disease (IBD) characteristics including fevers and ulcers that responded to IL-1, TNF, or IL-12p40 blockade. Using cells from patients and two newly generated mouse models, we uncovered hyperinflammatory responses of ELF4-mutant macrophages to a range of innate stimuli. Mechanistically, Elf4 in macrophages both sustained expression of anti-inflammatory genes such as Il1rn and limited upregulation of inflammation amplifiers, including S100A8, Lcn2, Trem1, and neutrophil chemoattractants. Indeed, therapeutic Trem1 blockade reversed inflammation and intestine pathology in Elf4-mutant mice challenged with lipopolysaccharide in vivo. Thus, the ELF4 transcription factor restrains inflammation and protects against mucosal disease, a discovery with broad translational relevance for human inflammatory diseases such as IBD.

overall_design: Examination of transcriptional and chromatin organization differences between WT and Elf4-/- mice. 49 samples total, experiments were performed with minimum 3 samples per genotype.

first: Tyler

last: Paul

first: Bucklin

last: Molly


title: The alternative activity of nuclear PHGDH contributes to tumor growth under nutrient stress

city: Shanghai

first: Ke

last: Zheng

address: No. 1630 East Road

institute: Shanghai Jiao Tong University

summary: Here we show under glucose deficiency PHGDH is phosphorylated by p38 at Ser371, which promotes the cytosol-localized PHGDH translocation into the nucleus. Meanwhile, AMPK concurrently phosphorylates PHGDH-Ser55 and selectively increases PHGDH catalytic activity against malate oxidation, thus pushing the reduction of NAD+ towards NADH generation. In the nucleus, the altered PHGDH activity positively regulates NADH/NAD+ ratio and thus restricts NAD+ level, and thereby leads to repression of NAD+-dependent PARP1 activity. Moreover, PHGDH is found to be associated with Ser73-phosphorylated c-Jun and specifically inhibits PARP1-mediated c-Jun poly(ADP-ribosyl)ation, which accordingly led to the impaired c-Jun transcriptional activity against genes expression linking to cell growth inhibition.

overall_design: Transcriptome profile analysis in WT rPHGDH and rPHGDH S371A or rPHGDH S55A SW1990 cells under glucose deprivation

first: Yuhui

last: Jiang

first: Chunmin

last: Ma


title: Next-generation sequencing (NGS) analysis of GCA effects on BMSCs

status: Public on Jul 28 2021

city: changsha

first: CHANGJUN

last: LI

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

institute: Xiangya Hospital of Central South University

summary: In this study, we aimed to investigate the effects of Grancalcin (GCA) on bone marrow stromal cells (BMSC) differentiation.

overall_design: Two groups of PBS treated Control group and GCA treated group with 3 replicate, total 6 samples in sum, were collected and analyzed.

first: Chang-Jun

last: Li

first: Ye

last: Xiao

first: Mi

last: Yang

first: Xiang-Hang

last: Luo


title: CXCL1: A new diagnostic biomarker for human tuberculosis discovered using Diversity Outbred mice

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: More humans have died of tuberculosis (TB) than any other infectious disease and millions still die each year. Experts advocate for blood-based, protein biomarkers to help diagnosis TB, which is critical in high-burden countries. However, the protein biomarker pipeline is small. Here, we used the Diversity Outbred (DO) mouse population to address this gap, identifying five protein biomarker candidates. One biomarker, serum CXCL1, met the World Health Organization’s Targeted Product Profile for a triage test to diagnose active TB from latent M.tb infection (LTBI), non-TB lung disease, and normal sera in HIV-negative, adults from South Africa and Vietnam. To find the biomarker candidates, we quantified seven immune mediators and four proteins corresponding to a subset of highly expressed genes unique to progressor DO mice. Next, we applied statistical and machine learning methods to the data, i.e., 11 proteins in lungs from 453 infected and 29 non-infected mice. After searching all combinations of five algorithms and 239 protein subsets, validating, and testing the findings on independent data, two combinations accurately diagnosed progressor DO mice: Logistic Regression using MMP8; and Gradient Tree Boosting using a panel of 4: CXCL1, CXCL2, TNF, IL-10. Of those five protein biomarker candidates, two (MMP8 and CXCL1) were crucial for classifying DO mice; were above the limit of detection in most human serum samples; and had not been widely assessed for diagnostic performance in humans before. In patient sera, CXCL1 exceeded the triage diagnostic test criteria (>90% sensitivity; >70% specificity), while MMP8 did not. Using Area Under the Curve analyses, CXCL1 averaged 94.5% sensitivity and 88.8% specificity for active pulmonary TB (ATB) vs LTBI; 90.9% sensitivity and 71.4% specificity for ATB vs non-TB; and 100.0% sensitivity and 98.4% specificity for ATB vs normal sera. Our findings overall show that the DO mouse population can discover diagnostic-quality, serum protein biomarkers of human TB.

overall_design: At 8-10-weeks old, mice were infected with aerosolized Mtb strain Erdman bacilli (~100 in experiments 1 and 2; ~25 in experiments 3, 4, 5) using a CH Technologies nose-only exposure system. All mice were weighed at least twice per week, and examined daily for lethargy, respiratory distress, and body condition. Mice that met morbidity criteria (body condition score < 2; severe lethargy; or respiratory distress prior to 60 days of infection were euthanized immediately, i.e., progressors (previously termed “supersusceptible”). Mice that controlled infection were termed controllers (previously termed “not supersusceptible”).  37 lung RNA samples were of sufficient purity to be analyzed at the Boston University Microarray and Sequencing Resource Core Facility (Boston, MA).

first: Deniz

last: Koyuncu

first: Bülent

last: Yener

first: Gillian

last: Beamer


title: Gene expression data from murine cutaneous squamous cell carcinoma genomes induced by Sleeping Beauty transposon mutagenesis

city: Tampa

first: Michael

middle: B.

last: Mann

state: Florida

address: 12902 Magnolia Drive

department: Molecular Oncology

institute: H. Lee Moffitt Cancer Center and Research Institute

summary: Transcriptome analysis of mRNA samples from a cohort of mice with histopathologically diagnosed cutaneous squamous cell carcinoma.

overall_design: Tissues from flash frozen skin was collected at necropsy from 21 mice with cutaneous squamous cell carcinoma (11 males, 10 females) using the Affymetrix Mouse Genome 430 2.0 Array platform. Array data was processed using the RMA algorithm as implemented in the affy package for R. No techinical replicates were performed.

last: Black

first: Karen

first: Leslie

last: McNoe

first: Luxmanan

last: Selvanesan

first: Jerrold

last: Ward

first: Nancy

last: Jenkins

first: Neal

last: Copeland


title: Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells

first: Simona

last: Cristea

state: Massachusetts

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

summary: The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming.

overall_design: single cell RNA-seq was performed for 10 samples

first: Masaki

last: Yagi

first: Franziska

last: Michor

first: Konrad

last: Hochedlinger


title: A candidate causal variant underlying both enhanced cognitive performance and increased risk of bipolar disorder

city: St. Louis

first: Joseph

last: Corbo

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

summary: Bipolar disorder is a highly heritable mental illness, but the relevant genetic variants and molecular mechanisms are largely unknown. Recent GWASs have identified an intergenic region associated with both cognitive performance and bipolar disorder. This region contains dozens of putative fetal brain-specific enhancers and is located ~0.7 Mb upstream of the neuronal transcription factor POU3F2. We identified a candidate causal variant, rs77910749, that falls within a highly conserved putative enhancer, LC1. This human-specific variant is a single-base deletion in a PAX6 binding site and is predicted to be functional. We hypothesized that rs77910749 alters LC1 activity and hence POU3F2 expression during neurodevelopment. Indeed, transgenic reporter mice demonstrated LC1 activity in the developing cerebral cortex and amygdala. Furthermore, ex vivo reporter assays in embryonic mouse brain and human iPSC-derived cerebral organoids revealed increased enhancer activity conferred by the variant. To probe the in vivo function of LC1, we deleted the orthologous mouse region, which resulted in amygdala-specific changes in Pou3f2 expression. Lastly, ‘humanized’ rs77910749 knock-in mice displayed behavioral defects in sensory gating, an amygdala-dependent endophenotype seen in patients with bipolar disorder. Our study suggests a molecular mechanism underlying the long-speculated link between enhanced cognitive performance and neuropsychiatric disease.

overall_design: mRNA-seq in mouse brain

first: Susan

middle: Q

last: Shen


title: Establishment, Maintenance and Recall of Inflammatory Memory

status: Public on Jul 27 2021

first: Samantha

last: Larsen

address: 435 East 30th Street

institute: NYU School of Medicine

summary: Known for nearly a century, but through mechanisms that remain elusive, cells retain a memory of inflammation that equips them to react quickly and broadly to diverse secondary stimuli.  Using mouse epidermal stem cells as a model, we elucidate how cells establish, maintain and recall inflammatory memory. Specifically, we landscape and functionally interrogate temporal, dynamic changes to chromatin accessibility, histone modifications and transcription factor binding that occur during inflammation, post-resolution and in memory recall following injury. We unearth an essential, unifying role for the general stress-responsive transcription factor FOS, which partners with JUN and cooperates with stimulus-specific STAT3 to establish memory; JUN then remains with other homeostatic factors on memory domains, facilitating rapid FOS re-recruitment and gene re-activation upon diverse secondary challenges. Extending our findings, we offer a comprehensive, potentially universal mechanism behind inflammatory memory and less discriminate recall, phenomena with profound implications for tissue fitness in health and disease.

overall_design: ATAC-Seq, CUT&RUN, ChIP-seq

first: Christopher

middle: J

last: Cowley

first: Elaine

last: Fuchs


title: The evolution of MET and NRAS gene amplification as sequential acquired resistance mechanisms in a patient with EGFR mutation positive non-small cell lung cancer

city: AURORA

first: Robert

last: Doebele

state: CO

department: Medical Oncology

institute: University of Colorado-AMC

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: EGFR mutant non-small cell lung cancer patients disease demonstrates remarkable responses to EGFR targeted therapy, but inevitably they succumb to acquired resistance, which can be complex and difficult to treat. Analyzing acquired resistance through broad molecular testing is crucial to understanding the resistance mechanisms and developing new treatment options. We performed diverse clinical testing on a patient with successive stages of acquired resistance, first to an EGFR inhibitor with MET gene amplification and then subsequently to combination EGFR and MET targeted therapies. A patient-derived cell line obtained at the time of disease progression was used to identify NRAS gene amplification as an additional driver of drug resistance to combination EGFR/MET therapies. Analysis of downstream signaling revealed ERK activation that could only be eliminated by trametinib treatment, while Akt activation could be modulated by various combinations of MET, EGFR and PI3K inhibitors. Combination of an EGFR inhibitor with a MEK inhibitor was identified as a possible treatment option to overcome drug resistance related to NRAS gene amplification.

overall_design: We submitted the cell line for comparative genomic hybridization (CGH) to determine whether any copy number alterations could explain the combination resistance observed in the patient-derived cell line. The data revealed numerous copy number gains and losses across most chromosomes in the cell line, including evidence for chromothrypsis of chromosome 7, with the region containing the MET gene amplified, consistent with the clinical testing results

first: Tara

last: Peters

first: Peter

last: Brzeskiewicz

first: Hala

last: Nijmeh

first: Anh

middle: T

last: Le


title: Genome-wide small RNA sequencing of proliferative and replicative senescent human vascular smooth muscle cells and exosomes

city: Semenyih

first: Yuh-Fen

last: Pung

address: Jalan Broga

country: Malaysia

institute: University of Nottingham Malaysia

summary: We report high-throughput sequencing of small RNAs can compare the profiles between proliferative and replicative senescent human vascular smooth muscle cells and exosomes

overall_design: Examination of differentially expressed miRNAs of proliferative and replicative senescent hVSMCs and their exosomes.

first: Duong

last: Nguyen


title: Genome-wide gene expression analysis in 84 neurospheres derived from as many primary glioblastomas

city: Candiolo

first: Francesca

last: De Bacco

institute: Candiolo Cancer Institute

summary: Gene expression analysis of neurosphere from primary glioblastoma tissue

overall_design: Total RNA obtained from neurospheres. Gene expression profile has been performed to investigate biological properties in neurospheres isolated from independent patients

first: Carla

last: Boccaccio

last: Orzan


title: Transcriptomic profiles of type I/III interferon-responsive hair follicle subsets from ROSA26YFP_Mx1 and ADAM10;ROSA26YFP_Mx1mice

status: Public on Jul 26 2021

city: Bethesda

first: Keisuke

middle: Chris

last: Nagao

state: Maryland

address: 9000 Rockville Pike, Bldg 10, Rm12N240B

institute: National Institute of Arthritis and Musculoskeletal and Skin Diseases

summary: Inflammation triggered by viral infections can obscure tissue function. We utilized a model of systemic anti-viral immunity and found that the ADAM10-Notch signaling axis in type I/III interferon-responsive upper hair follicles (HF) was crucial for the expression of genes that regulated skin microbiota and protected HFs and its stem cell niche from inflammatory destruction.

overall_design: Transcriptomic changes in sorted YFP+ upper HF cells from ROSA26YFP_Mx1 and ADAM10;ROSA26YFP_Mx1mice 4 days after poly(I:C) induction.

first: Keiko

last: Sakamoto

first: Seon-Pil

last: Jin

first: Doyoung

last: Kim

first: Benjamin

last: Voisin


title: Recurrence biomarkers of triple negative breast cancer treated with neoadjuvant chemotherapy combined with anti-EGFR antibodies [Agilent]

city: New York

first: Yingjie

last: Zhu

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: To find metastatic recurrence biomarkers of triple negative breast cancer (TNBC) treated by neoadjuvant chemotherapy and anti-EGFR antibodies (NAT), we evaluated tumor genomic, transcriptomic and immune features, using MSK-IMPACT assay, gene arrays, Nanostring technology and TIL assessment on H&E. Six patients experienced a rapid fatal recurrence (RR) and other 6 had later non-fatal recurrences (LR). Before NAT, RR had low expression of 6 MHC class I and 13 MHC class II genes but were enriched in upregulated genes involved in the cell cycle-related pathways. Their TIL number before NAT in RR was very low (<5%) and did not increase after treatment. In post-NAT residual tumors, RR cases showed high expression of SOX2 and CXCR4. Our results indicate that high expression of cell cycle genes, combined with cold immunological phenotype, may predict strong TNBC resistance to NAT and rapid progression after it. This biomarker combination is worth validation in larger studies.

overall_design: Nucleic acids were extracted from frozen tumor tissue (pre-NAT samples) using AllPrep DNA/RNA mini kit (Qiagen France SAS, Courtaboeuf, France) according to the manufacturer’s protocol. RNA quality was verified using the 2100 BioAnalyzer (Agilent Technologies). The extracted material was sent to Helixio (Saint-Beauzire, France), where it was hybridized with gene arrays (Human SurePrint, Agilent Technologies France, Les Ullis, France).

first: Maurizio

last: Scaltriti

first: Jorge

middle: S

last: Reis-Filho

first: Nina

last: Radosevic-Robin


title: Analysis of single cell gene expression profile in hiPSC-derived NPCs

city: Tsukuba

first: Hiroaki

last: Tateno

address: Tsukuba Central 2, 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: Single-cell sequencing has emerged as an indispensable technology to dissect the cellular heterogeneity, but never been applied to integrated analysis of glycans and RNA. Using oligonucleotide-labeled lectins, we developed a sequencing-based method to jointly analyze the glycome and the transcriptome in single cells. Using the developed method, we analyzed the relationship between the two modalities of human induced pluripotent stem cells during the differentiation into neural progenitor cells.

overall_design: Ninety-six single cells (human iPS cells and neural progenitor cells) were sequenced by using RamDA-seq protocol.

first: Fumi

last: Minoshima

first: Haruka

last: Ozaki

first: Haruki

last: Odaka


title: Multi-species single-cell transcriptomic analysis of ocular compartment regulons

city: Singapore

first: Kiyofumi

last: Hamashima

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB)

summary: We constructed the first single cell atlas of the human, porcine and zebrafish ocular compartments and compared inter-species transcriptomic expression data in retinal cell populations. In the non-retinal cell populations, we identified putative adult stem cells present in the iris tissue. We created a disease map of genes involved in eye disorders across cells of posterior and anterior compartments of eye. We also probed the regulons of different cell populations, which included transcription factors (TFs) and receptor-ligand interactions and reveal unique directional signalling and cross-talks between ocular cell-types. Such regulons were checked for conservation across vertebrates including human, mouse, pig, zebrafish, and non-human primates to identify common core factors. Finally, we focused on one such transcription factor KLF7, which was conserved across species. After perturbing KLF7 gene expression during retinal ganglion cells (RGC) differentiation from human embryonic stem cells, we conclude that KLF7 plays a major role in maturation of RGC cells during differentiation.

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design: Single cell RNAseq of different celltypes of eye was done and transcription factor profiles were studied.

first: Pradeep

last: Gautam

first: Ying

last: Chen

first: Yingying

last: Zeng

first: Bar

last: Makovoz

first: Bhav

last: Parikh

first: Hsin

middle: Y

last: Lee

first: Katherine

middle: A

last: Lau

first: Xinyi

last: Su

first: Raymond

last: Wong

first: Woon-Khiong

last: Chan

first: Hu

last: Li

first: Timothy

last: Blenkinsop

first: Yuin-Han

last: Loh


title: Ovulation suppression protects against chromosomal abnormalities in mouse eggs at advanced maternal age

city: Vienna

first: Bart

middle: Johan H

last: Dequeker

address: Dr. Bohr-Gasse 3

institute: IMBA - Institute of Molecular Biotechology

summary: The frequency of egg aneuploidy and trisomic pregnancies increases with maternal age. To what extent individual approaches can delay the “maternal age effect” is unclear since multiple causes contribute to chromosomal abnormalities in mammalian eggs. We propose that ovulation frequency determines the physiological ageing of oocytes, a key aspect of which is the ability to accurately segregate chromosomes and produce euploid eggs. To test this hypothesis, ovulations were reduced using successive pregnancies, hormonal contraception and a pre-pubertal knockout mouse model, and the effects on chromosome segregation and egg ploidy were examined. We show that each intervention reduces chromosomal abnormalities in eggs of aged mice, suggesting that ovulation reduction delays oocyte ageing. The protective effect can be partly explained by retention of chromosomal Rec8-cohesin that maintains sister chromatid cohesion in meiosis. In addition, single-nucleus Hi-C (snHi-C) revealed a deterioration in 3D chromatin structure including an increase in extruded loop sizes in long-lived oocytes. Artificial cleavage of Rec8 is sufficient to increase extruded loop sizes, suggesting that  cohesin complexes maintaining cohesion restrict loop extrusion. These findings suggest that ovulation suppression protects against Rec8 loss, thereby maintaining both sister chromatid cohesion and 3D chromatin structure and promoting production of euploid eggs. We conclude that the “maternal age effect” can be delayed in mice. An implication of this work is that long-term ovulation-suppressing conditions can potentially reduce the risk of Down’s syndrome pregnancies at advanced maternal age.

overall_design: In total, 126 snHi-C libraries were generated. We generated 20 snHi-C libraries from GV oocytes of C57BL/6J 2-2.5 month old (C57BL/6J_young) and 20 snHi-C libraries of C57BL/6J 14-18 month aged (C57BL/6J_aged) mice. We generated 12 snHi-C libraries from GV oocytes of C57BL/ICRFat 14-15 month aged virgin (ICRF_aged.virgin), 14 snHi-C libraries from GV oocytes of C57BL/ICRFat 14-15 month aged constant-mated (ICRF_aged.mated) mice and 11 snHi-C libraries from C57BL/ICRFat GV oocytes of 2-2.5 month old (young). We generated 49 snHi-C libraries from Rec8TEV/TEVWaplfl/fl (Tg)Zp3-Cre GV oocytes (n(-TEV) = 21 and n(+TEV protease) = 28).

first: Emmanouella

last: Chatzidaki

first: Sean

last: Powell

first: Johanna

last: Gassler

first: Mariana

last: Silva

first: Kikuë

last: Tachibana


title: Recurrence biomarkers of triple negative breast cancer treated with neoadjuvant chemotherapy combined with anti-EGFR antibodies [Nanostring]

first: Yingjie

last: Zhu

first: Maurizio

last: Scaltriti

first: Jorge

last: Reis-Filho

first: Nina

last: Radosevic-Robin


title: Systematic investigation of cytokine signaling activity at the tissue and single-cell levels

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

summary:
Purpose:  The role of different TGF-beta isoforms in tumor progression is not well established.  The goal of the study was to assess the effect on the 4T1 mouse mammary tumor transcriptomes of treatment with isoform-selective anti-TGFbeta neutralizing antibodies to address whether sparing TGF-beta3 had any biological impact.
Methods: 40,000 4T1 cells were implanted in the #4 mammary fatpad of syngeneic female BALB/c mice.  Mice were treated with therapeutic or control antibodies (5mg/Kg i.p. 3x q wk) for 12 days prior to tumor harvest for RNA-Seq analysis. Treatments were:  1D11 pan-TGFbeta mouse monoclonal, XPA.42.681 pan-TGFbeta human monoclonal, XPA.42.089 anti-TGFbeta1+2 human monoclonal, anti-KLH control human monoclonal, 13C4 control mouse monoclonal, or vehicle control.  Tumor mRNA profiles were generated by deep-sequencing of n=5 to 7 samples/treatment group using Illumina HiSeq2500 with TruSeq v4 chemistry.
Results:  51-115 million pass-filtered reads were obtained for all samples, with >=91% of bases having a quality score of 30 or above.

overall_design: mRNA profiles of 4T1 mouse mammary tumors treated with isoform-selective anti-TGFbeta antibodies were generated by deep sequencing of n=5-7 samples/treatment group by Illumina HiSeq2500

first: Peng

last: Jiang

first: Yu

last: Zhang

first: Beibei

last: Ru

first: Yuan

last: Yang

first: Trang

last: Vu

first: Rohit

last: Paul

first: Amer

last: Mirza

first: Grégoire

last: Altan-Bonnet

first: Lingrui

last: Liu

first: Eytan

last: Ruppin

first: Lalage

last: Wakefield

first: Kai

middle: W

last: Wucherpfennig


title: Embark cross-sectional study of inactive and active lesions from the ileum and colon of inflammatory bowel disease patients

city: South San Francisco

first: Jason

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

summary:
Hypothesis: Gene expression differences in biopsies from patients with inflammatory bowel disease can be used to identify molecular heterogeneity within patients with active disease.
Methods: Patients with a diagnosis of Crohn's disease, ulcerative colitis or normal healthy controls (with or without infectious colitis) underwent ileocolonoscopy. In healthy controls, biopsies were taken in the sigmoid colon (n=21), ascending/descending colon (n=25) and the terminal ileum (n=12). In patients with Crohn's disease, biopsies were taken in the ascending/descending colon (n=107) and terminal ileum (n=70) in uninflamed areas in all patients; in patients with mucosal lesions, additional biopsies were taken in inflamed regions of the ascending/descending colon (n=35) and terminal ileum (n=55). In ulcerative colitis patients, paired uninflamed sigmoid (n=48) and inflamed sigmoid biopsies (n=46) were taken. Biopsies were placed in RNAlater at the clinical site, frozen and shipped to Genentech, where they were disrupted using TissueLyzer beads, then RNA was isolated using RNeasy columns. RNA was hybridized to Agilent human 4x44kv1 arrays, dual channel, using universal reference.

overall_design: Intestinal biopsies were collected from active lesions and inactive adjacent regions in patients with either Crohn's disease or ulcerative colitis. Matched non-IBD controls with no obvious intestinal disease are included for comparison.

first: Mary

last: Keir


title: Use of Human Adult Stem Cell-Derived Organoid Cultures to Model Enterohepatic Circulation

city: Houston

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

summary: Organ to organ interactions have not yet been modeled with human organoid cultures. This work demonstrates the coupling of intestinal and liver organoids recapitulates aspects of enterohepatic bile signaling. The integration of organoids can be used to probe intra-organ interactions. Single cell RNA-Seq studies were performed in human liver organoids to examine the heterogeneity of the cultures.

overall_design: Liver organoids from three independent individuals were used for single-cell RNA-sequencing (scRNA-Seq).

first: Sarah

last: Blutt

first: Sue

last: Crawford

first: Betty

last: Slagle

first: Carolyn

last: Bomidi

first: Xi

middle: L

last: Zeng

first: Matthew

middle: R

last: Robertson

first: Cristian

last: Coarfa

first: Steven

last: Curley

first: F

middle: B

last: Hollinger

middle: K


title: Glutamatergic dysfunction precedes neuron loss in cerebral organoids with MAPT mutations

first: Alison

last: Goate

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Antimicrobial immunity impedes CNS vascular repair following brain injury

first: Kory

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Traumatic brain injuries (TBI) and cerebrovascular injuries are leading causes of disability and mortality worldwide. Systemic infections often accompany these disorders, which can impede recovery and significantly worsen outcomes. Remodeling of the central nervous system (CNS) after injury is essential for functional recovery and depends on temporally and spatially coordinated innate immune responses; however, the effect of systemic infections on this process is not well understood. Here, we demonstrate that a broad range of systemically introduced microbes and pathogen-associated molecular patterns interfered with immune-mediated meningeal vascular repair after TBI, with sequential infections promoting a prolonged state of disrepair. Mechanistically, we discovered that MDA5-dependent detection of a noncytopathic arenavirus encountered after TBI disrupted pro-angiogenic programming in recruited myeloid cells via local induction of type I interferon signaling. Systemic viral infection similarly promoted type I interferon-dependent impairment of restorative angiogenesis in the brain parenchyma after intracranial hemorrhage, leading to chronic blood brain barrier leakage, sustained interferon signaling, and a failure to restore cognitive-motor function. Our findings reveal an immunological mechanism by which systemic infections deviate reparative programming after CNS injury and offer a new therapeutic target to improve recovery and prevent states of prolonged neurological decline.

overall_design: Bulk RNA-Seq profiling of the cerebral cortex from twelve different mice in total; including four uninjured mice (Ctrl), four naïve cerebrovascular injured mice (CVI) at day 20 post-injury relative to uninjured mice, and four  cerebrovascular injured mice at day 20 post-injury relative to uninjured mice infected with lymphocytic choriomeningitis virus (CVI LCMV).

first: Panagiotis

last: Mastorakos

first: Mathew

middle: V

last: Russo

first: Tianzan

last: Zhou

first: Dorian

last: McGavern


title: Glutamatergic dysfunction precedes neuron loss in cerebral organoids with MAPT mutations [scRNA-Seq]

summary: Frontotemporal dementia (FTD) due to MAPT mutation causes pathological accumulation of tau and glutamatergic cortical neuronal death by unknown mechanisms. We used human induced pluripotent stem cell (iPSC)-derived cerebral organoids expressing tau-V337M and isogenic corrected controls to discover early alterations due to the mutation that precede neurodegeneration. Mutant organoids show early upregulation of MAPT expresssion and glutamatergic signaling pathways, as well as regulators including the RNA-binding protein ELAVL4. By 6 months, tau-V337M organoids show specific loss of glutamatergic neuronsof layers affected in patients. Mutant neurons are susceptible to glutamate toxicity, which was rescued pharmacologically by treatment with the PIKFYVE kinase inhibitor apilimod. Our results demonstrate a sequence of events that precede cell death, revealing molecular pathways associated with glutamate signaling as potential targets for therapeutic intervention in FTD.

overall_design: We performed cell hashing Single Cell sequencing on three isogenic pairs of cerebral organoids at 2, 4 and 6 months of differentiation, derived from patient iPSC lines carrying the MAPT V337M mutation, and CRISPR-corrected controls

first: Kathryn

last: Bowles

middle: M

first: Sally

last: Temple


title: Glutamatergic dysfunction precedes neuron loss in cerebral organoids with MAPT mutations [bulk RNA-Seq]

overall_design:
We performed bulk RNA-sequencing on three isogenic pairs of cerebral organoids at 2, 4 and 6 months of differentiation, derived from patient iPSC lines carrying the MAPT V337M mutation, and CRISPR-corrected controls
Samples 'S_72a01_4mo_b3_4' and 'S_6a02_4mo_b3_3' were outliers in 3D PCA, thereby removed in the downstream analyses

first: Yiyuan

last: Liu


title: Modelling HNF1B-associated monogenic diabetes using human iPSCs reveals an early stage impairment of the pancreatic developmental program

city: Autonomous CIty of Buenos Aires

first: Santiago

middle: Andres

last: Rodriguez Segui

address: Intendente Guiraldes s/n

country: Argentina

institute: IFIBYNE-UBA-CONICET

summary: Heterozygous mutations in HNF1B in humans result in a multi-system disorder, including pancreatic hypoplasia and diabetes mellitus. The underlying mechanisms that contribute to disease pathogenesis remain largely unknown, partially accounted by the fact that mouse models with heterozygous deletions in Hnf1b do not develop diabetes, in contrast to the phenotypes observed in MODY patients. Here we used a well-controlled human induced pluripotent stem cell pancreatic differentiation model to elucidate the molecular mechanisms underlying HNF1B-associated diabetes and pancreatic hypoplasia. Our results show that lack of HNF1B blocks specification of pancreatic fate from the foregut progenitor stage, but HNF1B haploinsufficiency allows differentiation of multipotent pancreatic progenitor cells and insulin secreting β-like cells. We further report that HNF1B happloinsuffiency impairs cell proliferation in foregut and multipotent pancreatic progenitors (MPCs). Our analyses suggest that this could be attributed to impaired induction of key pancreatic developmental genes, including FOXA1, SOX11, ROBO2, and additional TEAD1 target genes whose function could be associated with MPCs self-renewal. Taken together, these analyses have uncovered an exhaustive list of potential HNF1B gene targets during human pancreas organogenesis whose downregulation might underlie HNF1B-associated diabetes onset in humans, thus providing an important resource to understand the pathogenesis of this disease.

overall_design: We generated hIPSC lines carrying loss of function mutation in the HNF1B gene and then differentiated the resulting cells into pancreatic b-like cells in vitro.

first: Ranna

last: El-Khairi

first: Evelyn

last: Olszanowski

first: Daniele

last: Muraro

first: Pedro

last: Madrigal

first: Katarzyna

last: Tilgner

first: Mariya

last: Chhatriwala

first: Sapna

last: Vyas

first: Crystal

last: Chia

first: Andrew

last: Hattersley

first: Ludovic

last: Vallier

last: Rodríguez-Seguí


title: Characterization of Ppy-lineage cells clarifies the functional heterogeneity of pancreatic beta cells in mice

city: Maebashi

first: Yoshio

last: Fujitani

state: Gunma

address: 3-39-15 Showa-machi,

department: Developmental Biology and Metabolism

institute: Institute for Molecular and Cellular Regulation

summary: Pancreatic polypeptide (PP) cells, which secrete PP encoded by the Ppy gene, is a minor population of endocrine cells in the pancreas. At present, little is known about the characteristics of Ppy-expressing cells. Using a Ppy-Cre driver, here we show that cells of the Ppy lineage contribute to four major types of endocrine cells, including beta cells. Unbiased single-cell analysis with a Ppy-lineage tracer demonstrated that beta cells are composed of seven clusters, which are categorized into two groups; i.e., Ppy-lineage and non-Ppy-lineage beta cells. These subpopulations of beta cells demonstrated distinct characteristics in terms of functionality and gene expression profiles. Ppy-lineage beta cells are less active in glucose-stimulated calcium signaling, are localized at the periphery of islets, and survive for long periods in experimental diabetes models, and sharing various molecular characteristics with PP cells. Our results indicate the unexpected degree of beta-cell heterogeneity defined by Ppy-gene activation, providing valuable insights into the homeostatic regulation of pancreatic islets, and future therapeutic strategies against diabetes.

overall_design: scRNA-seq (10× Genomics Chromium Single Cell 3′ Solution v3.1) of islets from 8-week-old (postnatal day 56) healthy male MIP-GFP; Ppy-Cre; Rosa26-tdTomato mice with a mixed background of C57BL/6J and CD-1.


title: Regeneration of dermal papilla stem cells and mesenchymal components during feather cycling

city: Los Angeles

first: Ping

last: Wu

address: 2011 Zonal Ave HMR313A

department: Pathology

institute: University of Southern California

summary: Perform bulk RNA-seq in two groups of samples. Group 1 (sample 1 to 12) , Four dermal components in Early Growth phase feather follicle. Group 2 (sample 13 to 21), Pulp in different developmental stages.


title: Genome-wide mapping of H3K27ac and H3K9ac in platinum sensitive and resistant epithelial ovarian cancer cell lines

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

country: Germany

institute: University Stuttgart

summary: ChIP-seq for H3K27ac or H3K9ac was performed in different platinum sensitive and resistant epithelial ovarian cancer cell lines and in sensitive A2780 cells with shRNA induced knockdown of MBD3.

overall_design: H3K27ac ChIP-seq in A2780, A2780cis, CAOV4, CAOV4cis cells and A2780 cells with a control or two MBD3 shRNAs. H3K9ac ChIP in A2780 and A2780cis cells.

first: Tabea

last: Bauer

first: Katrin

last: Collmar


title: The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination

city: New Haven

first: Helen

middle: Alexander

last: Beilinson

address: 300 Cedar Street

department: Immunobiology

institute: Yale University

summary: Studies of novel RAG1 N-terminal region mutants reveal a role for the first 215 amino acids in establishing the balance between short- and long-range V(D)J recombination and a distinct role for RAG1 ubiquitin ligase activity in promoting efficient recombination and lymphocyte development.

overall_design: We generated mice in which RAG1 lacks ubiquitin ligase activity (P326G), the major site of autoubiquitination (K233R), or its first 215 residues (d215). We analyzed the Igh repertoire of these mice in bone marrow (B220+ IgM-) and splenic (B220+) B cells using HTGTS-Rep-seq with Jh1 and Jh3 as baits.

first: Anurupa

middle: D

last: Yadavalli

first: Jianxiong

last: Xiao

first: Elizabeth

last: Corbett

first: Huseyin

last: Saribasak

first: David

middle: G

last: Schatz


title: DNA methylation alternations in the offspring brown adipose tissue from high fat diet dams

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

summary: Maternal high fat diet may disturb susceptibility in offspring. Brown adipose tissue from maternal high fat diet has CpG sites that exhibit differential DNA methylationregulated compared to control.

overall_design: We performed DNA methylation array analyses of offspring brown adipose tissue from high fat diet dams and control diet dams (n=3 per group).

first: Xinhua

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Tong

last: Wang

first: Xiaojing


title: scRNAseq of human oligodendrocytes in primary culture exposed to glutamate vs. vehicle

status: Public on Jul 25 2021

city: Montreal

first: Olivier

last: Tastet

address: 900 Saint-Denis

institute: crCHUM

summary: T helper (Th)17 cells are considered to contribute to inflammatory mechanisms in diseases such  as multiple sclerosis (MS). However, the discussion persists regarding their true role in patients. Here, we visualized central nervous system (CNS) inflammatory processes in models of MS live in vivo and in MS brains and discovered that CNS-infiltrating Th17 cells form prolonged stable contact with oligodendrocytes. Strikingly, compared to Th2 cells, direct contact with Th17 worsened experimental demyelination, caused damage to human oligodendrocyte processes and increased cell death. Importantly, we found that in comparison to Th2 cells, both human and murine Th17 cells express higher levels of the integrin CD29, which is linked to glutamate release pathways. Of note, contact of human Th17 cells with oligodendrocytes triggered release of glutamate. As we found that Th17-polarized cells release glutamate in contact with oligodendrocytic cells, we then assessed the impact of glutamate itself on human oligodendrocytes in primary culture. We found that 12-24h application of glutamate - but not pro-inflammatory cytokines TNFα or IFN-γ - strongly decreased the area and complexity of human oligodendrocyte processes in vitro without affecting oligodendrocyte survival. To further investigate the impact of glutamate on human oligodendrocytes we used single cell RNA sequencing (scRNAseq) of the human oligodendrocytes in primary culture, unstimulated (vehicle) and stimulated with glutamate. Following exposure to glutamate we observed induced cell stress and changes in biosynthesis of cholesterol and lipids in mature human oligodendrocytes. Finally, exposure to glutamate decreased myelination whereas blockade of CD29 preserved oligodendrocyte processes from Th17-mediated injury. Our data provide first evidence for direct and deleterious attack of Th17 cells on the myelin compartment and show the potential for new therapeutic opportunities in MS.

overall_design: Two different batches, corresponding to two different donors in total. Each batch consisted of human oligodendrocytes in primary culture derived from the same brain sample (resection path of surgery for epilepsy) exposed to glutamate 1mM vs. vehicle for 12h.

first: Catherine

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